diff --git a/etcdserver/server.go b/etcdserver/server.go
index 6874405c6..0b446e4f4 100644
--- a/etcdserver/server.go
+++ b/etcdserver/server.go
@@ -208,6 +208,10 @@ type EtcdServer struct {
 	forceVersionC chan struct{}
 
 	msgSnapC chan raftpb.Message
+
+	// wg is used to wait for the go routines that depends on the server state
+	// to exit when stopping the server.
+	wg sync.WaitGroup
 }
 
 // NewServer creates a new EtcdServer from the supplied configuration. The
@@ -536,6 +540,8 @@ func (s *EtcdServer) run() {
 		s.r.stop()
 		sched.Stop()
 
+		s.wg.Wait()
+
 		// kv, lessor and backend can be nil if running without v3 enabled
 		// or running unit tests.
 		if s.lessor != nil {
@@ -1089,7 +1095,10 @@ func (s *EtcdServer) applyConfChange(cc raftpb.ConfChange, confState *raftpb.Con
 func (s *EtcdServer) snapshot(snapi uint64, confState raftpb.ConfState) {
 	clone := s.store.Clone()
 
+	s.wg.Add(1)
 	go func() {
+		defer s.wg.Done()
+
 		d, err := clone.SaveNoCopy()
 		// TODO: current store will never fail to do a snapshot
 		// what should we do if the store might fail?
diff --git a/storage/backend/backend.go b/storage/backend/backend.go
index 24fef1ad5..2625e4d7d 100644
--- a/storage/backend/backend.go
+++ b/storage/backend/backend.go
@@ -201,6 +201,18 @@ func (b *backend) Commits() int64 {
 }
 
 func (b *backend) Defrag() error {
+	err := b.defrag()
+	if err != nil {
+		return err
+	}
+
+	// commit to update metadata like db.size
+	b.batchTx.Commit()
+
+	return nil
+}
+
+func (b *backend) defrag() error {
 	// TODO: make this non-blocking?
 	// lock batchTx to ensure nobody is using previous tx, and then
 	// close previous ongoing tx.
@@ -251,8 +263,6 @@ func (b *backend) Defrag() error {
 	if err != nil {
 		log.Fatalf("backend: cannot begin tx (%s)", err)
 	}
-	// commit to update metadata like db.size
-	b.batchTx.commit(false)
 
 	return nil
 }
diff --git a/storage/backend/batch_tx.go b/storage/backend/batch_tx.go
index cea903c3f..24817b3c4 100644
--- a/storage/backend/batch_tx.go
+++ b/storage/backend/batch_tx.go
@@ -160,6 +160,8 @@ func (t *batchTx) commit(stop bool) {
 	// commit the last tx
 	if t.tx != nil {
 		if t.pending == 0 && !stop {
+			t.backend.mu.RLock()
+			defer t.backend.mu.RUnlock()
 			atomic.StoreInt64(&t.backend.size, t.tx.Size())
 			return
 		}